The folder are unified, but each acts completely independently.

I think right click the relevant "real" folder, select properties and then check the folder is set to get messages when the account is polled. It is not set by default for Junk/Spam and deleted/trash folders by default so your unified folder is probably not getting a "refresh when you delete because of it.

I right-clicked on the individual folders under the unified Deleted folder and selected the properties. In the general information tab and the retention policy tab, I don't see a get messages option. I saw a repair folder option, so I clicked that. Deleted messages started appearing when deleted from the main window pane using the delete button on the keyboard. As soon as I clicked on the trash can icon, it stopped working regardless of using the icon of the keyboard button. Haven't been able to get it working since, even if I repair the folders again. However, I ran repairs on the Inbox folders and deleted items are starting to appear again. Hopefully it holds.